Two different transitivity relationships. (a) Protein A and protein B share sequence identity of 34%, and protein B and protein C share sequence identity of 27%, whereas protein A and protein C only share sequence identity of 12%. We infer the homologous relationship between A and protein C through protein B. (b) Protein A and protein C are aligned with protein B1 and protein B2. The peptide fragments of B1 and B2 besieged by the rectangles are identical, the two corresponding peptide fragments of A and C are considered to be similar.